The left button is usually used to choose a class, a key (an
object is accessed through its key), or a button option.
Picking once highlights a class or key, and implements a button
option. Picking a class or key twice, or picking it once and
pressing Return, respectively displays the class's keys or the
key's object.
The middle button is only used to move around maps (see Sections 2
and 3).
When the word pick is used below it should be understood as
meaning to pick the left mouse button twice, unless
otherwise stated.
The class whose keys are to be listed should be picked once in
the ACEDB Class Window before the keys to be listed are
specified in the Template box. When the keys have been
specified either press return, or pick the class a second
time, to get the listing.
An asterisk in the text entry box represents any characters
e.g. to get a listing of all the unc loci, type unc* in
the Template box.
The default setting for the Template box is an asterisk. Hence
by default every key in the highlighted class is listed.
This is used to search all classes for a particular piece of
text. A list of the keys whose objects contain the text is given
in the Main Keyset Window.
Long Search
An entry in the Text Search Text Entry box is usually
only searched for among short pieces of text in a class's objects.
However, if the "Long Search" button is pressed long pieces
of text, such as abstracts, are also searched.
The search takes a bit longer than usual.
Process Box
This is the box to the right of the word "Classes" in the
ACEDB Classes Window. This box indicates the state of a process. For
instance, if a listing of authors is requested, the box will turn
red while the request is being processed. Once the process
is completed the box will revert to its usual green colour and
contain the word "Ready".
Menu For ACEDB Class Window
- Quit
- quits ACEDB
- Help
- provides context-sensitive help
- Clean Up
- closes all windows other then this one
- Program Status
- provides information about the program
- Add update file
- used to add data files when starting up the system
- Query
- used to do complex queries - see section 6 for details
- Query by Examples
- provides a more user-friendly way to do complex
queries, but dosen't contain all
the query capabilities as yet.
- Tablemaker
- used to create data tables
- DNA analysis
- This is the same as the Analysis
option in the Feature Map which will
be explained in Section 5.
If you are a privileged user some extra items appear on the
menu if you type "setenv ACEDB_SU" on the command line before
starting ACEDB.
- Add/Alias/Rename
- This provides a window in which you
create or delete an object
(e.g. an author),
change an object's key name,
or give a key an alias.
- Read Ace Files
- When data needs to be added to
the system, ace files are used. This
option enables you to read in
these files.
- Align Maps
- brings up a window that lets
you remake the maps after new data
has been entered
- Read Models
- to change database structure
- beware!
- Session Control
- used to start/rename/destroy
sessions
- Dump
- dumps out all the data in the system
- Write Access
- To change any data within the
system you need write access.
Keyset Windows
A keyset is simply a set of keys. The second window which appears
when you start up ACEDB is the "Main Keyset Window".
This usually contains the list of keys requested in
the "Template" text entry box of the ACEDB Class Window.
To see a key's object, such as a paper and its related data, pick
the key. A window will now appear. This will contain a series of
tags, such as Year and Volume, together with their data. When a piece of
data is in boldface format, the data is itself a key for an
object. If this key is picked, a window containing its object will
be displayed.
If only one key is requested in the "Template" section of the
ACEDB Class Window, the object of the single key in the keyset is
usually automatically displayed.
When a locus, rearrangement, clone or sequence key is selected, however,
its object's tags and data are not shown directly.
Instead, keys for loci and rearrangements are displayed in the appropriate
position on the genetic map and keys for clones and sequences are shown
in the appropriate position on the physical map.
In these cases, if the key on the map is picked, the key's
object will appear.
If you want to see a key's object without
having to bring up a map first, choose the "Show all text" option on
the keyset menu.
If a chromosome key is picked, the genetic map for that chromosome
is displayed. The only way to see the chromosome's textual data is
to use the "Show all text" menu option.
Other keysets can also be created. The number of keys in a keyset
is listed at the the top left of the keyset. The user can move from
one key to another using either the mouse or the arrow keys. He/She
can also scroll through a large listing rapidly using the page up and
page down button options.
When you pick the centre of the top of a keyset it becomes
the "Selected Keyset" (Selected Keyset appears at the top of the
window). The Selected Keyset has special significance for various
keyset calculations. The calculations are implemented using the
pull-down menu, activated when the window is picked once with the
right mouse button.
Menu For Keyset Windows
- Quit
- closes this window
- Help
- provides context-sensitive help
- Add keys
- This is used to add or delete keys
from this keyset.
- Copy
- creates a new keyset window with the same
keys as the current keyset
- Save
- saves a keyset
- AND
- lists keys which are common to the
current keyset and the Selected
Keyset
- OR
- lists keys in the current keyset and/or
the Selected Keyset
- MINUS
- lists keys in the current keyset less those
in the Selected Keyset
- XOR
- lists keys which are in the current keyset or
the Selected Keyset but not both
- Ace Dump
- dumps out the keys in the keyset
together with their related tags and data
- ASN Dump
- Ignore
- Name Dump
- dumps out the keys listed in the keyset
- Sequence Dump
- This is used to load a sequence into a file.
A sequence key should be highlighted before
this option is selected.
- Show as Text
- This displays a key's object.
It's useful for bypassing the map display
usually given when a locus, rearrangement,
sequence, chromosome, or clone is picked.
The relevant key in the keyset should be
highlighted before this option is selected.
- Show Related Biblio
- This shows the bibliography for a particular
key's object. The relevant key should be
highlighted before this option is selected.
Section 2: Genetic Map
The Genetic Map is used to display any genetically-mapped data,
including loci, rearrangements, multi-point and 2-point-data, and
balancers. A representation of the physical map is also included, as
are cloned loci, even in cases where they have no genetic mapping
data, to facilitate the intersection of the two maps.
Accessing the Genetic Map
Pick a chromosome in the ACEDB Class Window or a keyset window.
Alternatively pick a locus or rearrangement and the area of the map
containing it will appear.
Features of the Genetic Map Window (from left to right)
- Locator and Marker Loci
- The Locator is a vertical black line containing a
green bar. The black line represents the
whole chromosome and the green bar
indicates which part of the
chromosome can be seen to the right of the line.
Some loci are marked on the Locator to give the
user a rough idea where things are positioned
on the chromosome.
- Rearrangements
- Single lines are deficiency rearrangements, double
lines are duplication rearrangements. If you pick
one, a window will appear with information about
that rearrangement.
- Contigs
- The yellow bars show the Physical Map contig(s)
for the chromosome being examined.
- Loci without mapping data
- The loci shown between the contigs and the scale are
on the physical map but have not got genetic mapping data.
- Scale
- The units are centimorgans.
- 2_point_data and Multipoint data
- This can only be seen when the
GMap data button (see below) is used.
- Loci
- Those highlighted in yellow are cloned. If you
pick a locus a window will appear with information
about the locus.
Moving around the map
The zoom in/out buttons at the top of the page can be used to
increase or decrease the amount of the chromosome shown.
The Locator can also be used to zoom in and out. In this case you pick
the green bar with the middle mouse button and drag to
the left or right to zoom in or out respectively. You can
also use the Locator to move up and down the chromosome. In this case,
pick the green bar with the left button and drag it up or down.
Picking with the middle mouse button anywhere to the
right of the Locator produces a horizontal line which can be
dragged up or down the scale. This is used to indicate the place on
the scale where the data displayed should be centred. To scroll
through screenfuls of the map rapidly, position the horizontal line at
the top or bottom of the window and pick the line repeatedly.
Ways of accessing mapping data
Pick a locus and get the textual details about its
rearrangement, 3-point and 2-point data.
To get a graphical representation of a locus's mapping data,
highlight a locus and choose the GMap Data button option.
Rearrangements which are now highlighted in green
include the locus; those highlighted in blue do not.
Any 3-point or 2-point-data relating to the locus
is also shown. 3-point-data is represented as a vertical
line with a small square box for each of the three
loci. 2-point-data is the same except that there are 2 boxes.
Highlight a rearrangement and choose the GMap Data option.
Loci which are then highlighted in green are covered
by the rearrangement; those highlighted in blue are not.
Ways of getting to the Physical Map from the Genetic Map
Pick a locus which has yellow highlighting and
then pick the clone within that locus.
Alternatively, pick the contig. This will show the Physical Map
representation of what was being shown on the Genetic Map. The map
will be centred at the position you picked. There are little markers
on the contig which indicate the positions of the cloned loci
on the contig.
Genetic Map Buttons
- Columns
- This produces a list of various types of objects
which can be displayed on the genetic map, such
as rearrangements and multi point data. Those with
blue highlighting are displayed on the
map. Pick an object to add or remove highlighting.
- Whole
- shows the current map in its entirety
- Zoom In/Out
- decreases/increases the map area displayed
- Highlight
- highlights any loci and rearrangements
in the Selected Keyset
- GMap Data
- shows mapping data for the currently highlighted
locus or rearrangement
Genetic Map Menu
- Quit
- closes the map
- Help
- provides context-sensitive help
- Print Screen
- prints what is currently shown in this window
- Print Whole Map
- prints the whole map
- Preserve
- When a new map is created, the current map will be
preserved instead of being overwritten.
- Recalculate
- is used to recalculate the map when new map
position data for loci or rearrangements is added.
- Save Map
- is used to save any changes made to the map
- Hide Header
- is used to get rid of the button options and the blue
information bar at the top of the map.
Physical Chromosome Map
This feature shows the physically mapped objects of the chromosome. A
vertical black line represents the chromosome. Contigs are shown by
default, as yellow bars. The user can choose to have physically
mapped h as cDNAs, and cloned loci, displayed. The
objects users must import from a keyset (see "Physical
Chromosions" below), are represented as small boxes.
You can move around the map in the same way you can move around the
genetic map (see "Moving around the Map" above).
Physical Chromosome Map Buttons
- Whole
To bring up the entire chromosome
- Zoom In/Out
increases/decreases the amount of
the map shown
- Clear
clears any data imported from a keyset
Physical Chromosome Menu options
- Quit
- closes the map
- Help
- provides context-sensitive help
- Print
- prints what is displayed in
this window
- Preserve
- The current map will be preserved
instead of being overwritten when
a new map is created.
- Recalculate
- is used to recalculate the map
when new physical map data is added.
- Highlight Selectec Objects
- highlights any units on the
map which are in the Selected
Keyset.
- Add Selected Objects
- imports and displays any
physically-mapped units
which are in the Selected Keyset
- Subtract Selected Objects
- removes any physically-mapped
units in the Selected
Keyset from the map.
- Full Genome Distribution
- This shows all the chromosomes.
- Change Symbol Size
- changes the size of the boxes
representing physically-mapped units
- Change Bump Sloppiness
- changes the way boxes line up to
the right
Section 3: Physical Map
Accessing the Physical Map
The Physical Map can be accessed via the Genetic Map (see section 2)
or by picking a particular clone in the ACEDB Class Window or a
keyset window.
Features of the Physical Map (from the bottom up)
- Locator
- This consists of a black line showing the backbone of
the physical map and a green bar which indicates
the part of the map displayed above. Cloned loci
are marked on the black line as an extra guideline.
- Text
- These are remarks about the map and can be picked for
further information.
- Genetic Map bar
- Pick this bar to go to the Genetic Map (the position
is interpolated between the two nearest cloned loci).
Loci are marked and can be picked for
further text information.
- Pairs of small vertical lines
- These mark the position where cosmid
"islands" are bridged by a YAC. They indicate
that the length of the separation between the
two islands is unknown.
- Sequence Boxes
- These yellow boxes represent areas which have been
sequenced. If you highlight a sequence the related
clone and cloned locus (if there is one) will also be
highlighted. If you pick it a second time the
Feature Map (ie the sequence analysis window) will appear.
- Cosmids, cDNAs and YACs
- Cosmids and YACs are represented by horizontal lines.
cDNAs are simply positioned on the map.
All clones can be picked for text information.
Cosmids with asterisks have other cosmids buried
underneath them.
YACs represented by boldface horizontal
lines are gridded, i.e. we have polytene filter
information for them which can be probed with cDNAs etc.
Note: The arrow keys can be used to move from one clone, locus or
remark to the next.
Moving around the map
The Locator can be used to zoom in and out. Pick the green bar
with the middle mouse button and drag up or down to respectively
increase or decrease the amount of the map displayed. The
Locator can also be used to move left or right. Pick the
green bar once with the left button and drag to the
left or right.
Picking with the middle button anywhere above the Locator
produces a vertical line which can be dragged left or right.
This is used to indicate where the data displayed should
be centred. You can scroll screenfuls to the left or right by
picking repeatedly with the middle mouse button at the far
left or right of the screen.
Physical Map Menu
- Quit
- closes this window
- Help
- provides context-sensitive help
- Print
- prints the contents of this window
- Preserve
- The current map will be preserved instead of being
overwritten when a new map is created.
- Redraw
- Ignore
- Recalculate
- Used to recalculate the map when new physical map
data is added.
- Show all Remarks
- This shows extra, less relevant, remarks. Select
again to get rid of the remarks.
- Show Selected Objects
- restricts the clones on the map to those
in the Selected Keyset
- Highlight Selected Objects
- highlights those clones on the map which are in
the Selected KeySet
- Unhighlight/Revert
- removes highlighting from any loci or
rearrangements on the map which are also in the
Selected Keyset
- Show All Buried Clones
- shows all the clones that are "underneath" the
canonical ones
- To Genetic Map
- If a locus or clone has been highlighted, this option
will display the genetic map at the locus's
or clone's estimated position.
- Sequence
- shows the sequence for the highlighted clone
- Set Zoom
- changes the size of the zoom
- Set Display Depths
- Here you can specify the number of lines used for
each type of data. For instance, if you had a lot of YACs
and very few cosmids you might choose to increase
the number of lines for showing YACs.
Section 4: Clone_Grid Window
This display represents a high-density gridded filter. It can
show hybridisation information for probes to a filter, and
is used both to view data and enter it. In the worm ACEDB there
is a filter POLY1 of representative YACs, and cDNA clones have been
mapped via this to the physical map.
How to access the clone grid
The grid can be accessed by choosing the Clone_Grid option on the
ACEDB Class Window menu.
What You See
You see a window with small boxes representing YACs. The YACs are
laid out in the way they are organized on the filter.
If you highlight one of them you get the name of the yac in the
Gridded Clone text entry box at the top of the window.
If you type the name of a yac in the Gridded Clone text entry box
then the small box on the filter which corresponds to that yac will
light up.
If you pick the Gridded Clone button itself you can then pick a yac
in a keyset or the physical map menu and if it is on the filter
it will be highlighted.
If you want to test where a cDNA hybridises to the grid, type
the name of the cDNA in the Probe text entry box at the top left
of the window.
If you pick the Probe button itself you can then pick a
probe, such as a cDNA, on the physical map or a keyset,
and if it hybridises to the filter the relevant small boxes
will be highlighted.
There are two modes of action for double clicks on the boxes
themselves:
Map Mode: if you double-click on a box you will see the
corresponding location on the physical map. If the box was lit
positive then any other positive neighbouring yacs will be
combined in to define a single map location.
Edit Mode: when you click on a square you change the colour
of the square. This lets you enter a hybridisation signal.
It is also possible to use pooled probes rather than single clone
probes. This uses items in the Pool class (not used in worm
ACEDB).
Menu for Clone Grid
- Quit, Help, Print, Preserve
- as normal
- Centre <-> Surround
- Lets you save the current pattern as
a background for comparison with other
hybridisation patterns.
- Toggle name display
- Shows full names of all clones in grid.
Too big for screen but good for printing.
- Toggle small display
- Displays at life size for the filter, to
allow overlaying of film during data entry.
- Set small sizes
- Sets the dimensions of the small display
to allow accurate overlaying.
- Display probe as tree
- Like "Show as text" in keyset menu
- Save data with probe
- To store a hybridisation pattern with
a probe (the one named in the probe box).
Requires write access.
- Set cluster range
- Lets you set a value that determines how
the map position is calculated for a probe
that hits overlapping clones. If there
is a gap bigger than this value then
multiple map positions are registered.
- Stats on keyset
- Given that a keyset of probes is the
selected keyset, this says how many map
loci are defined by their hybridisation
patterns, etc.
- Change gridded clone
- To edit the clone grid object (requires
write access).
Section 5: Sequence Display
This is the most complex display window in the ACEDB package, with
many options. To get to it select any sequence object, or a yellow
bar in the physical map.
It resembles the genetic map window in general organisation. The
direction of display is from top to bottom. Scrolling and zooming
are achieved exactly as with the genetic map. In the main,
information is only shown for the positive strand. The strand can
be reversed and/or complemented using a pull-down menu from the
"Reverse-Complement" button (press the right mouse button when the
pointer is inside the button).
Many different types of information can be shown. Which are
available at any one time are controlled by the Columns
button.
Display Control
- Columns
- This button switches the screen to a menu screen that lets you
pick which columns of information are displayed. Options are,
in top to bottom order:
- Locator
- Bar representing whole sequence with green cursor
showing current location
- Clones
- names and extents of cosmids sequenced
- Up Genes
- Splicing pattern of genes on the opposite strand,
running bottom to top.
- Restriction map
- when you look for a "Motif" in the analysis window,
the names of the matches are shown in the matching
positions in this column
- Summary bar
- Yellow bar that is used to show locations of features
- Scale
- Shows coordinates with respect to current origin.
- Down Genes
- Splicing pattern of genes on the positive strand.
- Temp_gene
- The working gene when using genefinder.
- Finished
- different levels of hatching indicate different levels
of completion of the genomic sequence. Not very useful
because not currently kept up to date.
- CDS Lines
- show a horizontal line for each CDS = Coding Sequence
= predicted gene. For use when zoomed right out, to see
over all distribution.
- CDS Boxes
- like CDS lines, but a different shape symbol. Lines are better.
- cDNAs
- shows the cDNAs as small black boxes
- Gene names
- names of genetically defined genes that correspond to
predicted sequences, in the correct vertical positions
- Assembly Tags
- data imported from the xbap sequence assembly database
- under development
- 3 Frame Translation
- as it says
- ORF's
- Shows stop codons in each frame as horizonal lines.
- Coding Frame
- For a predicted gene, shows the frame of each exon.
- ATG
- Shows all ATG's as small yellow boxes. After getting
Genefinder features the width of the box varies
according to the log probability of being an initiator
methionine codon.
- Coding Potential
- Shows regions of high coding potential as grey boxes.
The width depends on the likelihood of being coding.
- Peptide Similarity
- Rectangles show regions of BLASTX similarity to
database proteins in the appropriate frame. The width
varies according to score (significance).
- Gene Translation
- The translation of the currently selected gene. You
must be selecting a gene, or an intron or exon for
this to work.
- DNA Similarity
- Regions of BLASTN similarity to DNA sequences.
- Inverted Repeats
- as it says
- Tandem Repeats
- as it says
- User Segments
- a facility for reading in a file of features from an
outside program, defined by a sequence name, start
and end positions in the sequence and a score. These
are drawn as yellow rectangles, with the width
depending on score.
- Splices
- Used to show Genefinder predictions of splice sites.
3' and 5' sites are differentiated by directional hooks.
Length is proportional to log significance level.
- Coords
- Coordinates for the DNA.
- DNA Sequence
- The DNA sequence itself. Whenever any other feature is
picked the corresponding DNA region is highlighted.
- Brief_Identifications
- gives a short description (a word or two) for the type
of proteins that a predicted gene matches
- Text Features
- Any text attached to the sequence, including EMBL
annotation etc.
Other control features
The Origin data entry box at the top of the window allows you to reset
the origin by typing in a relative position. Also, if you click on the
Origin button you can then click on any feature in the window, and
its startpoint will become the new origin (e.g. a predicted gene, or
an exon).
The "Active zone" is the region in which various analytical
tools will operate, such as searches for restriction sites.
It is also the region that will be written out as a sequence
file by the "Export Sequence" menu option. You can change it by typing
new values into the text entry box at top right (don't forget
to hit return). The bounds of the active zone are shown by
blue lines adjacent to the yellow summary bar.
There is a light blue reporting row below the
active zone box and above the buttons that shows information
about the currently selected object.
The Genefinder submenu operates like the Reverse-Complement
submenu described above, and gives access to the Genefinder
prediction package of Phil Green. The details of this package
are beyond this manual.
The Clear button removes any highlighting and clears the
summary bar.
Sequence menu
- Quit, Help, Print Screen/Whole Map, Preserve
- as normal
- Recalculate
- This is used to recalculate the map when new
data has been added.
- Clear DNA
- Equivalent to the Clear button.
- EMBL dump
- Only for the C. elegans sequencing project
(unfortunately).
- Hide header
- Hides the header for pretty printouts.
- Color exons
- If a gene is selected and the DNA is being
displayed then this highlights all the exons
and introns in the DNA sequence in alternating
green and yellow.
- Export translation
- If a gene is selected this appends the
translation of the gene to a file in FASTA
format.
- Export translations
- dumps to a file the translations of all
predicted coding sequences in the current active zone
- Export Sequence
- Writes out the DNA sequence for the current
active zone to a user defined file.
- Statistics
- Prints out a summary of all features for the
current sequence to the standard output.
- Read User Segments
- read in the data to be displayed in the "User
segments" column (see Columns above)
- Analysis window
- Starts the DNA analysis package in a new window.
DNA Analysis Window
This is either accessed from the last entry of the sequence
display menu, or from the "DNA" entry of the ACEDB Class Window menu.
It provides various forms of simple DNA sequence analysis,
either applied to a single sequence in the current sequence
display window, or to whole sets of sequences defined by a
keyset. This choice of single sequence or keyset is
controlled by the toggle button at top. There is another
toggle on the right between DNA and AA (amino acids). Many
features only work for DNA.
The text entry line (yellow) allows you to type a simple
search pattern (using IUPAC nucleotide codes) or the name of
a restriction enzyme (from the Restriction class downloaded
from Rebase -- Rich Roberts). You can in fact type several
patterns, separated by semicolons. The cutpoints will be
shown below in the analysis window, and if you are working
with a single sequence the sites will be highlighted on the
summary bar and in the displayed sequence.
Other functions are accessed by buttons, as below:
- Finger print
- Restricts with the enzymes used for the worm physical map
HindIII and Sau3aI. The sites are shown in 2 colours in the
feature window.
- Motif Key_Set
- Will import a list of motifs that can then be
searched for in the active sequence or keyset of sequences.
- Max mismatch
- If this is not zero, it allows an approximate match of the
sequence to the motif (restriction site). The value is the number of
allowed mismatches. e.g. attgcc matches atagcc if "Max mismatch" is
set to 1 (or more).
- Dump Sequence
- If UseKeySet is set, dumps in fasta format all sequences of
the active keyset (the Selected Keyset).
Else, dumps in fasta format the active region of the active
sequence window, e.g. you can fasta dumps bases 3800 to 7000 of a
given sequence.
- EMBL dump
- This dumps any EMBL data for the active sequence or keyset of
sequences into a file.
- Splice Concensus
- Gives the 5' and 3' splice concensus sequences around the
introns exons boundaries in the sequences of the active
keyset. The result is shown in the analysis window itself.
Resize the window to see it.
- Codon Usage
- Gives the codon usage in the sequences of the active
keyset. The result is shown in a new window. Note that the
genetic code is accessible via the online help package.
- Sequence Lengths
- Gives the histogram of the lengths of the individual
sequences in the active KeySet.
- Show gels
- Pops a Gel Tool with its own help page.
- Clear
- Clears the Dnacpt window, useful before using Splice
concensus or restrict buttons.
Section 6: Query Window
There are currently two query options in the main ACEDB window menu.
One, "Query by example" is very user_friendly but has not got the
full range of capabilities at present. The second "Query" is slightly
less user friendly but has all the query capabilities. This
section deals with Query but I have included a small section on Query
by Example at the end.
General Comments
Queries are used to list keys and their data with particular
conditions attached.
Conditions are stated on command lines which are activated when picked.
If the bottom command line is edited a new empty one will appear. You
can combine various commands by joining them with semi-colons; the
result of each command is passed into the next one. Typing new
commands on each line and activating them separately will give the
same result (if the same keyset is used throughout).
If we specify a class on the command line all members of that
class will be examined for the stated conditions relating to them and
their tags. If we specify a tag without giving a class then all the
class members currently in the selected keyset will be examined.
Output is directed to the Selected Keyset.
Syntax
If you want a class searched put either of the following:
"Find Classname" or ">?Classname".
A tag, such as the Paper tag within the Author class, should be
simply stated as "Tagname" if you want a list of all the class keys which
have something in that tag.
However if you want the actual data for a key's tags you should
say ">Tagname". See examples one and two below.
The conditions given should become progressively more
specific. For instance, you might put a class
first, then the conditions pertaining to the name of keys
in that class, then a tag within that class, and lastly
the conditions pertaining to the tag.
The following operators can be used in queries.
In order of precedence:
| OR in either (union)
^ XOR in one or the other but not both
& AND in both (intersection)
! NOT
Some tags have subfields to their right in a key window. The
NEXT command is used to access these (see Example 8 below).
The HERE command is used for multiple checks on the one spot (see
Example 9 below).
The COUNT command counts what is to the right. See example 5 below.
Parentheses such as "(" or "[" can be used but must be matched.
The conditions given for tags or classes must have double quotes if
the text includes any of the following: & | ^ < > = ( ) [ ] { }
EXAMPLES
1
>?Author (or FIND Author)
In this case a class is given without any qualifying
conditions, so each member of the class will be listed.
2 (a)
Paper
No class has been specified, only a tag within a
class. Hence keys of any class (within the Selected Keyset)
are examined, but only those containing a paper will be listed.
(b)
>Paper (or FOLLOW Paper)
This is similar to 2(a) but in this case rather than
showing the items that contain papers, we show the
papers they contain.
3
>?Author s*|a*
In this case it's specified that only members of the author
class whose name begins with s or a should be listed
4
>?Paper Journal=Nat* AND Year > 1987
Here, in addition to specifying the class Paper, we're giving
conditions for data in the tags Journal and Year within
the Paper class's keys. The papers of interest are those
in journals beginning with Nat and whose year of publication
is later than 1987.
5
>?Locus myo* Clone
In this case we're interested in the Locus class keys
whose title begins with myo* and whose the locus class keys
contain clones. As indicated before, if a tag, such as Clone,
is stated without any conditions attached then all members
of the class which have something in this tag are included.
6
>?Author IS "Sulston JE"; >Paper; >Author
Here we have a combination of commands. The result of each
command feeds into the next. The aim is to get the
authors who collaborated on papers with John Sulston.
The three commands are as follows:
The first gives the key Sulston JE.
The second command gives all the papers for the key resulting
from the first command, so we get all the papers by Sulston JE.
The third command gets all the authors for the keys resulting
from the second stage, so we get all the authors for papers
by Sulston JE .
7
>?Author COUNT Paper > 10
This will list all authors who have more than 10 papers
recorded in ACEDB.
8
>?Locus gMap = X AND NEXT > 12
NEXT is used to locate a subfield to the right of a tag.
In this case we're looking for keys in the Locus class which
contain X in the gMap (i.e. chromosome name) tag. Also the gMap
tag's subfield, namely the Position field immediately to its
right, which we get by using the command NEXT, should contain a
position which is greater than 12.
9
>?Locus gMap = X AND NEXT > 12 AND HERE < 19
This is similar to Example 8 except for the last part.
The command HERE lets us give a second condition to the field
currently being examined (in this case the Position subfield).
Hence, only keys whose gMap Position subfield is both greater
than 12 and less than 19 will be listed.
Query Menu
- Quit
- Quits this window with an option to save your current
set of commands
- Help
- provides context-sensitive help
- Print
- prints this window
- Clear entries
- clears the current instructions on the command lines
- New Keyset
- opens a new keyset window
- Query by Example
- see below
- Load from File
- loads a previous set of instructions from a file
- Save to File
- saves the current set of commands to a file
- Search Locally
- Implements the search
- Send
- Ignore
- Undo
- cancels the last command and redisplays the previous keyset
The button options are the same as the menu options.
Query by Example
Query by Example, as stated earlier, is very user friendly but hasn't
got the full range of query capabilities. The following is a brief
description of how it can be used.
First indicate what you want the search done on, a whole class of
objects or a keyset of objects, by toggling the button with the
word "From:" to its right.
Then indicate the class to which the objects should belong, by
selecting an item to the right of the word "Class:". The selection can
be made by toggling through the classes, or by picking the Class: button with
the right mouse button and choosing from the resulting list of
classes. Tags and data fields for that class will appear below.
Then it is necessary to indicate any limitations you want to place on
the objects to be listed. If you are only interested, for instance, in
finding Papers which have an entry in their Abstract tag, pick the
Abstract tag. If you want to look at papers which have a particular kind
of entry in a particular tag then you must type the condition in the green
box to the right of the relevant tag. For instance, if you were only interested
in Papers which have an entry beginning with Nat in the Journal tag,
type Nat* in the green box to the right of the Journal tag.
Lastly, pick the "Search Locally" button to see the result.